The Matrix: Rewritten
by Narehs
Summary: The Agents have been rewritten. Though the males are finding their new directive easy. The female agents are starting to resist the change. Caught in the middle is Ms. Johnson. An original Agent from the beginning like Mr. Smith. After a female agent destroys an entire city. They are all recalled. Soon Ms. Johnson finds herself as the leader of a growing resistance...
1. Introduction

**Disclaimer: ** I do not own the Matrix.

_Hey All! I've recently been enjoying the Matrix story and I got to thinking... Why aren't there any female agents? Guess I'll just have to write a story about it ;) A short introduction whilst I work on a couple of chapters. Enjoy! xo Naz_

**Introduction**

There was a time in the Matrix where all wishes were answered, all dreams came true. I was most happy during this era. Agents were protectors. Minimising the death of humans. We weren't even called Agents back then. We were Peace Keepers.

Happiness... I know right... How can a computer program be happy?

I honestly don't know. What else can I call that bubbly feeling in my chest? That tempting need to smile? It can't be anger... or hatred. The outcomes of those emotions would be different.

Like all happiness that I've come to observe within the Matrix, my own didn't last long.

This dream world of unicorns and faeries. Of rainbows and sunshine soon turned sour. And my happiness along with it.

Humans rejected this first attempt at a programmed reality. Entire crops destroying themselves through disbelief. A stupid species. But then, wasn't that why we were created?

None the less, this disaster inspired a reboot. This time the Matrix didn't just manifest desires and dreams, but fear and nightmares as well. Soon vampires and werewolves were programmed in. Monsters of all imaginations stepping into our reality.

Though the humans did not reject this reality, the death toll was too high.

We tried our best. But these horrors were stronger. Faster. In some cases, smarter. All the Agents, including myself, received an upgrade to match the imaginations of humans. But we couldn't be everywhere all at once.

So a second reboot occurred. We were wrong altogether to give humans the control over their reality. We fixed this mistake with a simple algorithm.

The Architect, with the help of the Oracle, chose a specific time in human history, the year 1999. Only after setting programs were in place, and the Train Master installed were humans once again plugged in. This time the Matrix was cold, almost cruel, mimicking the world by way of recorded history.

Control taken. The only remaining elements, virtual as they are, were hope and choice. Some humans were even set free from the Matrix altogether to create a human colony below the surface called Zyon.

It was in this moment Agents went from protectors to policers. Out directive was to control at all costs.

Machines finally had success. Human crops flourished. But we didn't.

How could we? Agents were written with the sole purpose to protect humans. Now we were to kill them? A simple patch could not stop our purpose. And out continual failures to police the unplugged humans were noticed.

So we were rewritten.

And that's where my story begins. When the train stops...


	2. Memory

**I guess going from Yautja to Matrix is quite a jump, but the plot of this story kept me up at night so I thought I'd get it down on paper. It's going to be a bumpy ride, full of twists and turns, so have fun reading. I'll try and get a chapter out every month. But I'm still finishing off my Al'kin story as well. **

**Chapter 1**

Screaming to a screeching stop, the train had me gripping the metal bar with all my strength to stay in one spot. My muscle, under my linen white long-sleeved blouse and black long-sleeved blazer, flexing so the rest of my body would look at peace. I wonder if the other agents had to do the same?

_Agents..._

The thought felt so foreign against my memories of the past. But it fit none the less. Only because I had been cut to fit this new mould, this new Matrix. We all had.

Even my partner, Smith, seemed different standing next to me. The lights over our head reflecting off the shiny black of his sun glasses.

His black suit and tie contrasting perfectly against his white shirt. I was dressed the same, instead of neat black pants, I wore a knee length skirt. We looked smart, we looked official, we looked professional. A smart, official, and professional killer.

That's right. I was a killer now. Or I was programmed to kill. The knowledge filling my head like water to a jug. Flowing easily to the front of my mind. Not only a killer, a great one at that.

_What about prote-_

I couldn't even finish the thought, my mind short circuiting to focus on a more pressing matter. The train had come to a complete stop. It was time to disembark.

The train driver was already on the platform, giving us a royal wave. Somehow an annoying ass had been programmed into his design.

_I could fix that, I could kill him. A simple flick of my-_

What the hell was I thinking? Before I could frown and self reflect, the agents pressing in on all sides started to move. I joined in, keeping to the right of Smith. Neither of us had spoken since the reboot of the last Matrix reality. Even after coming out of the tunnel from Source where our programming and individual coding gave way to our current bodies, silence still grew between us.

There were others around me I recognised from previous Matrix realities. Ms. Williams, Mr. Brown, Mr. Jones, Ms. Davis, Mr. Miller, Ms. Wilson, Ms. Taylor, Mr. Jackson, Ms. Lee. All wearing the required ear plug and black and white business suit, all faces were covered in tinted sunglasses that seem to mould their faces into merciless expressions. No one was smiling. No one was happy.

_Happy..._

My mind short circuited again, this time causing me pain. I stopped my hiss with a clench of my teeth. My instinct telling me to blend in, don't draw suspicion. I wasn't sure why, but I always trusted my instinct. It had led me right in the past. It would do so again.

That was when I wondered, what if my instinct had been rewritten as well? A question to ask Smith later. He had been the one to show me I had such a gift.

"Come on, hurry up. I know you're the Agents, but we haven't got all day." He did a mocking horror sound you would find in a movie of the same genre, waving his hands and rolling his eyes as we piled onto the platform. Such disrespect. I moved to intervene.

Smith grabbed my forearm quicker than a blink. Seems like we were even faster than before, or maybe just him. Another upgrade? Were we to meet more werewolves and vampires? "Allow me Johnson." Smith bowed his head politely.

He had finally spoken to me, it was relief that made me relax back into my watchful stance.

Smith moved forward going toe to toe with the train driver. The train driver hitched his chin, "You can't kill me. It's not your directive."

Tilting his head, I watched as Smith slowly sighed, "True, I cannot kill you." The train driver was already hitting the concrete wall of the underground train station before my mind had registered that Smith had punched the Entrance Program in the face.

The shabby man fell to the floor along with pieces of broken concrete. Dust rose with his impact on the ground. "But I can hurt you." Smith looked back at me, "Let's go."

I followed him to the stairwell, unsure if we were still partners like previous Matrix. When we reached the busy street, humans passed us by on all sides, none bumped into us know. Maybe instinctually they knew.

I looked to Smith, his glasses gleamed in the afternoon sun. I had so many questions, my mind swimming with thoughts I've never had before. Thoughts that weren't of my own design. Surprisingly my consciousness processed everything before I went crazy. Still, this new white noise was disheartening.

"Over there." Smith nodded towards a black 1965 Lincoln Continental waiting at the kerb.

Instead of moving forward like my partner did, I looked back. Were the others coming?

Lee and Jackson were the only Agents following from the station. I turned back to Smith, he was already falling into the passenger side seat, leaving the driving to me.

Stepping forward, humans passed around me like a frantic stampede to a tall tree.

Getting in I slammed the door, "Lee and Jackson joining us?"

"No, we have the CBD, they have the outskirts."

"And the others?" I turned the key, the engine purred to life. It was silly to ask the question, as soon as I thought about it, the information was streaming through my mind. But I needed to ask, I needed to talk. Needed to hear his voice. The reboot had happened so suddenly. I didn't get a chance to say goodbye.

I thought we were gone for good. Deleted. It wasn't until the train had come out of the tunnel and I found myself standing next to Smith I realised this wasn't the case.

"They've already assimilated to Plugs in other cities."

That's right. We could jump between humans. No... that wasn't right. Only one partner could jump. They hadn't been able to program strength with agility, movement with power. So we partnered up. One with strength. One with agility. While one was an unstoppable force. The other was an immovable object. The ultimate team.

We were both abnormally strong and fast, that was easy enough to program. But I just knew, I was faster. Smith was stronger. More than before the reboot. In the previous matrix, I could run a 100m in 10 seconds, even sustain that speed indefinitely. But now, I didn't have to run. I could jump in between the Plugs. Smith could only run.

"You can assimilate as well." The knowledge came to me like the breeze from the air con.

Smith looked at me his glasses reflecting my solemn gaze as I kept my focus on the road ahead. "Only through you."

More information assaulted me. Smith could only lock onto me, not Plugs. His program could push me out of a Plug, I would have to find another one. Fear then struck me. The choking cold grappling me as worry bloomed in the pit of my stomach. I knew the only way around fear was to voice it. "What if I leave a part of myself behind on each Jump?"

Smith hissed low, "Do not speak of these things."

I felt reprimanded. His response only fuelling the fear.

"Yet." His one word an almost inaudible whisper. Instantly relief cascaded through me. He was still the Smith from my memories. I had worried, truly worried that he had changed.

But if they hadn't taken away my emotions, fear included. Hopefully they hadn't taken away his.

We drove the rest of the way in silence. On occasion I would give a slight glance to Smith, who remained watchful and quiet looking out his window. Taking in the Matrix with new eyes.

Horrible thoughts filled my mind. _Like ants. Like disease. Like virus. _

Such hatred filled me. Fear and hatred, concern and worry. Was this to me my new life? Clenching my teeth, I mentally shook off these waring emotions and thoughts, focusing on getting to HQ instead. An office building located centrally in the city.

Each Agent team had their own location to work from within their own jurisdiction. I was guided easily enough by the information flowing through my mind. Turn here, turn there.

Even after parking in an underground garage, and moving into the lift, the silence between Smith and I remained in place. From his one word whisper, I gathered he was waiting for privacy to speak to me. So when the lift doors opened on our floor and new home, I waited for him to move first.

Removing his sunglasses, he stepped forwarded, turning right. As I followed suit, I glimpsed an open plan office to our left, full of analysts and human agents. That's right. Smith and I would head a division. Always searching for the unplugged humans. As much as Smith and I had, what humans would deem, 'god-like' abilities, the parasite tendencies of humans were advantageous in completing our directive.

Parasite tendencies? Where had that come from?

Coming to a door labelled 'Director', Smith moved through the grey flushed door, trailing after him, I closed it.

All in silence. A waiting silence. I was holding everything in. Like a breath I couldn't breathe out. My lungs on the verge of exploding. Smith moved further into the room. I couldn't follow any longer. Leaning against the cool door, I sighed, not daring to look up. Afraid I would find more cold silence. "Please tell me you remember?"

Smith laughed. A hate filled laugh. Why was there so much hate now?

I wanted to cry, fall to my knees and let my agony out. But I would wait for a response first. It was only seconds away, maybe minutes. I knew I had only just enough strength left for that.

He was facing the ceiling to floor window, the city stretching out for miles. In the distance, hills rolled and clouds blew low around them. Such a beautiful city. I winced as pain filled my mind again.

"You fight it?" It was only a blink of pain, yet Smith had turned to me and seen it. He saw everything. For some reason, I had been programmed differently to the other original Peace Kee –another shot of pain – Agents.

He had seen it then. And he saw it now. Maybe he had been programmed differently as well. Maybe he had one gigantic bull-shit detector.

"Of course I fight it." The call was strong. The voices loud. But my very essence was up for grabs. And I wouldn't let them win.

Slowly, so slowly he pulled the cream ear piece away and stalked towards me, stopping with only an inch separating our bodies. I didn't dare move. His navy blue eyes piercing through me. My breath deepened as his hand raised and pulled my own ear piece away. The voices went with it. My blink held for mere seconds in reprieve. Finally the white noise was gone. All that was with me was Smith.

Opening my eyes again I looked up at Smith. His focus following his hand as it moved from my ear to skim over my cheek. With a soft pinch he raised my chin, tilting my head slightly back. "I'm not sure how long I can fight my directive." He admitted in a whisper. His mouth leaning towards mine. "But I remember."

Our eyes clashed only for mere seconds before our mouths followed. His hold on my chin pulling me into his mouth. Moving quickly to cup the back of my neck, his hand fisting my hair, angling me for his taste. Our mouths duelled, our tongues flickering together like whips of fire.

Gripping his forearms, his expert kiss drew me to the edge of sanity itself. My hands snaking around his neck until our bodies pressed so tightly together we became one.

Suddenly he pulled from my mouth. I moaned, my grip tightening. My eyes flaring open in anger that he dare break our kiss.

He chuckled, "I remember everything."

I opened my mouth to respond, but he took it instead. My words turning into another moan as he kissed me into a frenzied oblivion.


End file.
